Multiple sequence alignment - TraesCS2D01G368800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G368800 chr2D 100.000 2792 0 0 1 2792 473274873 473277664 0.000000e+00 5156
1 TraesCS2D01G368800 chr2B 90.049 2854 169 51 1 2792 553612085 553614885 0.000000e+00 3591
2 TraesCS2D01G368800 chr2A 89.419 2807 170 53 46 2792 615343262 615346001 0.000000e+00 3421
3 TraesCS2D01G368800 chr1B 82.353 374 38 18 2137 2508 599469637 599469984 1.630000e-77 300
4 TraesCS2D01G368800 chr6B 77.376 221 39 7 1123 1342 476110916 476110706 1.360000e-23 121
5 TraesCS2D01G368800 chr6A 77.376 221 39 7 1123 1342 445581423 445581633 1.360000e-23 121


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G368800 chr2D 473274873 473277664 2791 False 5156 5156 100.000 1 2792 1 chr2D.!!$F1 2791
1 TraesCS2D01G368800 chr2B 553612085 553614885 2800 False 3591 3591 90.049 1 2792 1 chr2B.!!$F1 2791
2 TraesCS2D01G368800 chr2A 615343262 615346001 2739 False 3421 3421 89.419 46 2792 1 chr2A.!!$F1 2746

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
520 550 0.108662 GCGAAAAGGGCAATTGGAGG 60.109 55.0 7.72 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2160 0.603439 GGCAAACCAAACAGGCCATG 60.603 55.0 5.01 2.64 44.01 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.779733 TCCTCTCCACCCGCTCCC 62.780 72.222 0.00 0.00 0.00 4.30
37 38 2.752903 CCCCCTTGGTTTAGTCAAATCG 59.247 50.000 0.00 0.00 0.00 3.34
63 64 3.763360 TGTTTGGTCTTCCATGGCTAATG 59.237 43.478 6.96 0.00 43.91 1.90
156 159 0.322098 TCCACTATGCAAACCGTGGG 60.322 55.000 20.05 5.36 45.33 4.61
176 179 7.064609 CCGTGGGTACATATTATAGAATGCAAG 59.935 40.741 0.00 0.00 0.00 4.01
178 181 6.884295 TGGGTACATATTATAGAATGCAAGCC 59.116 38.462 0.00 10.53 33.67 4.35
193 196 1.244019 AAGCCGTGTTCCATGCCTTC 61.244 55.000 0.00 0.00 0.00 3.46
197 200 0.523072 CGTGTTCCATGCCTTCCTTG 59.477 55.000 0.00 0.00 0.00 3.61
268 271 2.750815 AGTCAAATACTGCGGCGTC 58.249 52.632 9.37 0.91 36.93 5.19
273 276 0.601576 AAATACTGCGGCGTCACACA 60.602 50.000 9.37 0.00 0.00 3.72
279 282 2.587753 CGGCGTCACACAGTGGTT 60.588 61.111 5.31 0.00 33.87 3.67
280 283 2.594962 CGGCGTCACACAGTGGTTC 61.595 63.158 5.31 0.00 33.87 3.62
281 284 2.251642 GGCGTCACACAGTGGTTCC 61.252 63.158 5.31 0.00 33.87 3.62
283 286 0.884704 GCGTCACACAGTGGTTCCAT 60.885 55.000 5.31 0.00 33.87 3.41
284 287 1.606994 GCGTCACACAGTGGTTCCATA 60.607 52.381 5.31 0.00 33.87 2.74
299 321 5.200483 GGTTCCATATCCTTGGTGATTCAA 58.800 41.667 0.00 0.00 38.01 2.69
326 348 5.915628 TCCCAGGAAGATATGCTAGGATAA 58.084 41.667 8.13 0.00 32.52 1.75
348 370 9.865321 GATAACATGTCAGTACAACCTAAAGTA 57.135 33.333 0.00 0.00 39.58 2.24
359 381 6.940430 ACAACCTAAAGTAGCTTAGGGTTA 57.060 37.500 12.76 0.00 45.07 2.85
471 494 1.904537 TCAGCCTGCTGAGAAAGATGA 59.095 47.619 17.46 0.00 46.80 2.92
520 550 0.108662 GCGAAAAGGGCAATTGGAGG 60.109 55.000 7.72 0.00 0.00 4.30
521 551 1.544724 CGAAAAGGGCAATTGGAGGA 58.455 50.000 7.72 0.00 0.00 3.71
522 552 1.474077 CGAAAAGGGCAATTGGAGGAG 59.526 52.381 7.72 0.00 0.00 3.69
630 666 2.691011 GTGGATAGACTCCTCAGGACAC 59.309 54.545 0.00 0.00 45.21 3.67
793 829 5.261216 TCCAACTCTTCTTTCTTGGTGTTT 58.739 37.500 0.00 0.00 35.58 2.83
811 847 9.802039 TTGGTGTTTTATCTAGTCCTTAAACAT 57.198 29.630 0.00 0.00 37.67 2.71
832 887 8.856153 AACATACAATTATAGGTGTGTTCACA 57.144 30.769 1.23 1.23 43.03 3.58
833 888 8.263940 ACATACAATTATAGGTGTGTTCACAC 57.736 34.615 22.85 22.85 45.45 3.82
850 905 9.011407 GTGTTCACACGTTATCAACATTTTAAA 57.989 29.630 0.00 0.00 37.10 1.52
851 906 9.011407 TGTTCACACGTTATCAACATTTTAAAC 57.989 29.630 0.00 0.00 0.00 2.01
879 934 6.173339 TCATGATTAGTCCCACTTTTCTGAC 58.827 40.000 0.00 0.00 0.00 3.51
880 935 5.825593 TGATTAGTCCCACTTTTCTGACT 57.174 39.130 0.00 0.00 40.87 3.41
881 936 6.187727 TGATTAGTCCCACTTTTCTGACTT 57.812 37.500 0.00 0.00 38.85 3.01
882 937 6.601332 TGATTAGTCCCACTTTTCTGACTTT 58.399 36.000 0.00 0.00 38.85 2.66
883 938 6.486657 TGATTAGTCCCACTTTTCTGACTTTG 59.513 38.462 0.00 0.00 38.85 2.77
909 967 8.154856 GCCTTTCCATTACATGTATTCCTACTA 58.845 37.037 6.36 0.00 0.00 1.82
924 982 3.656751 TCCTACTATCTACTGACCTCCCC 59.343 52.174 0.00 0.00 0.00 4.81
938 996 6.327887 ACTGACCTCCCCTTCTATTTCTATTC 59.672 42.308 0.00 0.00 0.00 1.75
962 1020 1.684450 TGCAGTACCGTGAGTTCTTCA 59.316 47.619 0.00 0.00 0.00 3.02
965 1023 3.799232 GCAGTACCGTGAGTTCTTCAACT 60.799 47.826 0.00 0.00 46.21 3.16
978 1036 6.119144 GTTCTTCAACTAGAACTGTTTGCA 57.881 37.500 0.00 0.00 46.69 4.08
981 1039 4.530094 TCAACTAGAACTGTTTGCAACG 57.470 40.909 0.00 0.00 0.00 4.10
982 1040 3.035942 CAACTAGAACTGTTTGCAACGC 58.964 45.455 0.00 0.00 0.00 4.84
1073 1131 1.899814 TCCAGTGTCCGATAACAAGCT 59.100 47.619 0.00 0.00 0.00 3.74
1098 1156 4.361783 TGAAGAACATCAGTGGGGAGATA 58.638 43.478 0.00 0.00 0.00 1.98
1102 1160 3.136641 ACATCAGTGGGGAGATACCTT 57.863 47.619 0.00 0.00 38.98 3.50
1113 1171 1.038130 AGATACCTTCAGCCGCGACT 61.038 55.000 8.23 0.00 0.00 4.18
1155 1219 1.160137 GCAACATCTGCCTCGACTTT 58.840 50.000 0.00 0.00 46.13 2.66
1188 1252 0.109723 TTGTTACCCTCTGTGGCCAC 59.890 55.000 29.67 29.67 0.00 5.01
1224 1288 1.589993 CATCTACGAGTGGCTGCGG 60.590 63.158 0.00 0.00 0.00 5.69
1275 1339 2.035421 CACTTCAGCAAGGCAGCAA 58.965 52.632 4.78 0.00 36.85 3.91
1362 1426 3.866651 CTCGAAGAAATCACTGGATGGT 58.133 45.455 0.00 0.00 34.09 3.55
1365 1429 5.624509 CTCGAAGAAATCACTGGATGGTACA 60.625 44.000 0.00 0.00 39.20 2.90
1407 1471 1.971167 GCACCGGGAGAATGTTGCA 60.971 57.895 6.32 0.00 0.00 4.08
1438 1502 1.528161 CGCAAAGCAGCATCGATGATA 59.472 47.619 29.20 0.00 0.00 2.15
1485 1549 2.363795 CCTCCACTCCGGCCACTA 60.364 66.667 2.24 0.00 33.14 2.74
1521 1585 1.077930 CCATCCTGGTGCCACTGAG 60.078 63.158 0.00 0.00 31.35 3.35
1859 1923 5.070001 GGCTTGTGTATATATTGGAAGGCA 58.930 41.667 0.00 0.00 35.30 4.75
1871 1935 4.712051 TTGGAAGGCATGATATACTGCT 57.288 40.909 0.00 0.00 38.45 4.24
1897 1961 5.178797 TCGAGGAAAAAGAAGGCAAGATAG 58.821 41.667 0.00 0.00 0.00 2.08
1901 1965 7.201565 CGAGGAAAAAGAAGGCAAGATAGTAAG 60.202 40.741 0.00 0.00 0.00 2.34
1908 1972 5.667626 AGAAGGCAAGATAGTAAGGAATGGA 59.332 40.000 0.00 0.00 0.00 3.41
1912 1976 6.064717 GGCAAGATAGTAAGGAATGGATGTT 58.935 40.000 0.00 0.00 0.00 2.71
1913 1977 6.016777 GGCAAGATAGTAAGGAATGGATGTTG 60.017 42.308 0.00 0.00 0.00 3.33
1914 1978 6.543831 GCAAGATAGTAAGGAATGGATGTTGT 59.456 38.462 0.00 0.00 0.00 3.32
1915 1979 7.067494 GCAAGATAGTAAGGAATGGATGTTGTT 59.933 37.037 0.00 0.00 0.00 2.83
1916 1980 8.400947 CAAGATAGTAAGGAATGGATGTTGTTG 58.599 37.037 0.00 0.00 0.00 3.33
1965 2029 5.741011 AGGAATGGTTAATGCTCTTAACGA 58.259 37.500 13.01 10.90 36.13 3.85
1990 2054 2.423926 ATCGGTAAGCATGCGTCTAG 57.576 50.000 10.11 4.26 0.00 2.43
2066 2130 2.430465 TCATTCTTGTCTTGCCTCAGC 58.570 47.619 0.00 0.00 40.48 4.26
2096 2160 5.099042 ACTCCATTACCTGAACCATACAC 57.901 43.478 0.00 0.00 0.00 2.90
2135 2200 2.169144 CCTGCATCTGTCACTACCATGA 59.831 50.000 0.00 0.00 0.00 3.07
2146 2234 6.173339 TGTCACTACCATGAGGATTTTCTTC 58.827 40.000 0.00 0.00 38.69 2.87
2185 2273 0.827925 TGCATTGGGTTGGCGGTTTA 60.828 50.000 0.00 0.00 0.00 2.01
2202 2290 5.409214 GCGGTTTACTGTTACTGGATTTACA 59.591 40.000 0.00 0.00 0.00 2.41
2203 2291 6.619232 GCGGTTTACTGTTACTGGATTTACAC 60.619 42.308 0.00 0.00 0.00 2.90
2230 2318 3.343617 TGAATCTCCCCATTCGTTGTTC 58.656 45.455 0.00 0.00 35.78 3.18
2232 2320 0.672401 TCTCCCCATTCGTTGTTCGC 60.672 55.000 0.00 0.00 39.67 4.70
2233 2321 0.953471 CTCCCCATTCGTTGTTCGCA 60.953 55.000 0.00 0.00 39.67 5.10
2323 2412 7.887996 TTGTAGATTTGCAAATTGAATGACC 57.112 32.000 24.81 10.16 0.00 4.02
2336 2426 2.102420 TGAATGACCCGAAGCATATCGT 59.898 45.455 5.96 0.00 41.16 3.73
2337 2427 3.319689 TGAATGACCCGAAGCATATCGTA 59.680 43.478 5.96 0.00 41.16 3.43
2341 2431 3.822167 TGACCCGAAGCATATCGTACATA 59.178 43.478 5.96 0.00 41.16 2.29
2342 2432 4.082949 TGACCCGAAGCATATCGTACATAG 60.083 45.833 5.96 0.00 41.16 2.23
2343 2433 3.825014 ACCCGAAGCATATCGTACATAGT 59.175 43.478 5.96 0.00 41.16 2.12
2347 2437 6.527023 CCCGAAGCATATCGTACATAGTAAAG 59.473 42.308 5.96 0.00 41.16 1.85
2348 2438 7.082602 CCGAAGCATATCGTACATAGTAAAGT 58.917 38.462 5.96 0.00 41.16 2.66
2349 2439 7.060748 CCGAAGCATATCGTACATAGTAAAGTG 59.939 40.741 5.96 0.00 41.16 3.16
2350 2440 7.590322 CGAAGCATATCGTACATAGTAAAGTGT 59.410 37.037 0.00 0.00 38.01 3.55
2354 2444 8.273557 GCATATCGTACATAGTAAAGTGTTTGG 58.726 37.037 0.00 0.00 0.00 3.28
2356 2446 4.931002 TCGTACATAGTAAAGTGTTTGGCC 59.069 41.667 0.00 0.00 0.00 5.36
2357 2447 4.691685 CGTACATAGTAAAGTGTTTGGCCA 59.308 41.667 0.00 0.00 0.00 5.36
2358 2448 5.179742 CGTACATAGTAAAGTGTTTGGCCAA 59.820 40.000 16.05 16.05 0.00 4.52
2359 2449 5.447624 ACATAGTAAAGTGTTTGGCCAAC 57.552 39.130 20.35 14.11 35.71 3.77
2361 2451 5.596772 ACATAGTAAAGTGTTTGGCCAACTT 59.403 36.000 20.35 16.84 36.21 2.66
2363 2453 7.285858 ACATAGTAAAGTGTTTGGCCAACTTTA 59.714 33.333 26.66 26.66 42.52 1.85
2366 2456 6.983890 AGTAAAGTGTTTGGCCAACTTTATTG 59.016 34.615 30.27 0.00 44.09 1.90
2367 2457 5.351948 AAGTGTTTGGCCAACTTTATTGT 57.648 34.783 20.35 0.00 36.21 2.71
2368 2458 6.472686 AAGTGTTTGGCCAACTTTATTGTA 57.527 33.333 20.35 0.00 36.21 2.41
2369 2459 6.084326 AGTGTTTGGCCAACTTTATTGTAG 57.916 37.500 20.35 0.00 36.21 2.74
2391 2481 8.668353 TGTAGATGTTGAGACATTTCAATTAGC 58.332 33.333 0.00 0.00 46.27 3.09
2419 2509 7.388500 GCCGTGCCCTACTTTATTGTATAATAA 59.612 37.037 0.87 0.87 37.06 1.40
2446 2536 2.877097 TGCCCAACTGCATCTTTCTA 57.123 45.000 0.00 0.00 36.04 2.10
2468 2558 3.144506 CACTGTGCAAGGAGAAGTCATT 58.855 45.455 0.00 0.00 0.00 2.57
2647 2737 8.682710 ACAATACTGATTATATTTGCAAACGGT 58.317 29.630 15.41 13.65 0.00 4.83
2669 2759 6.308766 CGGTGGCAAAATCTCAGAATTTTAAG 59.691 38.462 0.00 0.00 36.86 1.85
2673 2763 8.859090 TGGCAAAATCTCAGAATTTTAAGAGAA 58.141 29.630 0.00 0.00 40.19 2.87
2693 2783 7.989826 AGAGAATAAAACTGACCAATATGCAC 58.010 34.615 0.00 0.00 0.00 4.57
2752 2842 4.913335 ATAGCTCAATCCATTTGCACAG 57.087 40.909 0.00 0.00 35.16 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.392595 GACTAAACCAAGGGGGAGCG 60.393 60.000 0.00 0.00 41.15 5.03
18 19 2.163613 GCCGATTTGACTAAACCAAGGG 59.836 50.000 0.00 0.00 0.00 3.95
63 64 4.222114 GCTGTAATTGAATATTCAGCGCC 58.778 43.478 17.28 8.73 38.72 6.53
110 111 3.289834 CGTTTGCAGGTGCTGGCT 61.290 61.111 3.18 0.00 42.66 4.75
156 159 7.117812 ACACGGCTTGCATTCTATAATATGTAC 59.882 37.037 0.00 0.00 0.00 2.90
197 200 1.801765 CGGCTTAAGAGTTACCTCGGC 60.802 57.143 6.67 0.00 42.86 5.54
268 271 3.634397 AGGATATGGAACCACTGTGTG 57.366 47.619 7.08 1.06 0.00 3.82
273 276 3.189606 TCACCAAGGATATGGAACCACT 58.810 45.455 0.00 0.00 43.54 4.00
278 281 6.078456 ACTTGAATCACCAAGGATATGGAA 57.922 37.500 8.29 0.00 45.76 3.53
279 282 5.715439 ACTTGAATCACCAAGGATATGGA 57.285 39.130 8.29 0.00 45.76 3.41
280 283 6.183360 GGAAACTTGAATCACCAAGGATATGG 60.183 42.308 8.29 0.00 45.76 2.74
281 284 6.183360 GGGAAACTTGAATCACCAAGGATATG 60.183 42.308 8.29 0.00 45.76 1.78
283 286 5.222233 TGGGAAACTTGAATCACCAAGGATA 60.222 40.000 8.29 0.00 45.76 2.59
284 287 4.089361 GGGAAACTTGAATCACCAAGGAT 58.911 43.478 8.29 0.00 45.76 3.24
299 321 4.349342 CCTAGCATATCTTCCTGGGAAACT 59.651 45.833 3.55 0.00 33.34 2.66
326 348 6.014499 AGCTACTTTAGGTTGTACTGACATGT 60.014 38.462 0.00 0.00 34.86 3.21
348 370 7.829706 CCTCTTTGTTATTCTTAACCCTAAGCT 59.170 37.037 0.00 0.00 37.49 3.74
359 381 8.319146 TCCGTCTTTATCCTCTTTGTTATTCTT 58.681 33.333 0.00 0.00 0.00 2.52
383 406 0.950116 GGCTACAGATGCTGCATTCC 59.050 55.000 17.36 4.85 34.37 3.01
471 494 1.540367 TCCCCACGGAAGAACCCAT 60.540 57.895 0.00 0.00 34.19 4.00
520 550 6.422400 GTGCCAGAGAATAACTATAAGCACTC 59.578 42.308 0.00 0.00 41.64 3.51
521 551 6.127054 TGTGCCAGAGAATAACTATAAGCACT 60.127 38.462 0.00 0.00 43.43 4.40
522 552 6.049149 TGTGCCAGAGAATAACTATAAGCAC 58.951 40.000 0.00 0.00 43.38 4.40
630 666 3.576356 GCCCACGCCACATCATCG 61.576 66.667 0.00 0.00 0.00 3.84
709 745 2.772515 CCTAAAATTCGAGGGAGAGGGT 59.227 50.000 0.00 0.00 0.00 4.34
826 881 8.196241 CGTTTAAAATGTTGATAACGTGTGAAC 58.804 33.333 0.00 0.00 35.11 3.18
829 884 6.358558 AGCGTTTAAAATGTTGATAACGTGTG 59.641 34.615 0.00 0.00 40.12 3.82
831 886 6.904954 AGCGTTTAAAATGTTGATAACGTG 57.095 33.333 0.00 0.00 40.12 4.49
832 887 7.133513 TGAAGCGTTTAAAATGTTGATAACGT 58.866 30.769 0.00 0.00 40.12 3.99
833 888 7.541743 TGAAGCGTTTAAAATGTTGATAACG 57.458 32.000 0.00 0.00 40.71 3.18
834 889 9.123709 TCATGAAGCGTTTAAAATGTTGATAAC 57.876 29.630 0.00 0.00 0.00 1.89
835 890 9.853555 ATCATGAAGCGTTTAAAATGTTGATAA 57.146 25.926 0.00 0.00 0.00 1.75
836 891 9.853555 AATCATGAAGCGTTTAAAATGTTGATA 57.146 25.926 0.00 0.00 0.00 2.15
837 892 8.761575 AATCATGAAGCGTTTAAAATGTTGAT 57.238 26.923 0.00 0.00 0.00 2.57
838 893 9.340695 CTAATCATGAAGCGTTTAAAATGTTGA 57.659 29.630 0.00 0.00 0.00 3.18
839 894 9.128107 ACTAATCATGAAGCGTTTAAAATGTTG 57.872 29.630 0.00 0.00 0.00 3.33
840 895 9.341899 GACTAATCATGAAGCGTTTAAAATGTT 57.658 29.630 0.00 0.00 0.00 2.71
841 896 7.968405 GGACTAATCATGAAGCGTTTAAAATGT 59.032 33.333 0.00 0.00 0.00 2.71
842 897 7.432252 GGGACTAATCATGAAGCGTTTAAAATG 59.568 37.037 0.00 0.00 0.00 2.32
843 898 7.122055 TGGGACTAATCATGAAGCGTTTAAAAT 59.878 33.333 0.00 0.00 0.00 1.82
844 899 6.431543 TGGGACTAATCATGAAGCGTTTAAAA 59.568 34.615 0.00 0.00 0.00 1.52
845 900 5.941058 TGGGACTAATCATGAAGCGTTTAAA 59.059 36.000 0.00 0.00 0.00 1.52
850 905 2.501723 AGTGGGACTAATCATGAAGCGT 59.498 45.455 0.00 0.00 0.00 5.07
851 906 3.185246 AGTGGGACTAATCATGAAGCG 57.815 47.619 0.00 0.00 0.00 4.68
909 967 5.426325 AATAGAAGGGGAGGTCAGTAGAT 57.574 43.478 0.00 0.00 0.00 1.98
924 982 8.704234 GGTACTGCAATCGAATAGAAATAGAAG 58.296 37.037 0.00 0.00 0.00 2.85
938 996 1.654105 GAACTCACGGTACTGCAATCG 59.346 52.381 0.23 0.00 0.00 3.34
978 1036 1.605710 GCAATCAGGATGCTATGCGTT 59.394 47.619 3.68 0.00 40.64 4.84
1113 1171 3.196207 AAAGGAGCCGCTTCCAGCA 62.196 57.895 10.36 0.00 42.58 4.41
1155 1219 0.472044 TAACAACTGGGTCTGCAGCA 59.528 50.000 9.47 0.00 0.00 4.41
1188 1252 1.451028 GCAAGGCCAGCAGTAGAGG 60.451 63.158 14.58 0.00 0.00 3.69
1229 1293 2.425592 CGGAAGCTGACACCACCA 59.574 61.111 0.00 0.00 0.00 4.17
1236 1300 2.281484 TTGGCACCGGAAGCTGAC 60.281 61.111 9.46 0.00 0.00 3.51
1362 1426 1.813859 CCGTCGAGGAATGGCTGTA 59.186 57.895 6.70 0.00 45.00 2.74
1365 1429 4.162690 GGCCGTCGAGGAATGGCT 62.163 66.667 6.70 0.00 46.72 4.75
1407 1471 3.952675 CTTTGCGCGTGCTGGTGT 61.953 61.111 23.16 0.00 43.34 4.16
1438 1502 2.197324 ATTGTGGTGGTGCCGGTT 59.803 55.556 1.90 0.00 41.21 4.44
1859 1923 6.656632 TTTCCTCGAGAAGCAGTATATCAT 57.343 37.500 15.71 0.00 35.40 2.45
1871 1935 3.485463 TGCCTTCTTTTTCCTCGAGAA 57.515 42.857 15.71 3.49 0.00 2.87
1897 1961 5.391312 AAGCAACAACATCCATTCCTTAC 57.609 39.130 0.00 0.00 0.00 2.34
1901 1965 8.292448 CACTATATAAGCAACAACATCCATTCC 58.708 37.037 0.00 0.00 0.00 3.01
1908 1972 9.836864 TCTTCATCACTATATAAGCAACAACAT 57.163 29.630 0.00 0.00 0.00 2.71
1912 1976 8.363390 CCTCTCTTCATCACTATATAAGCAACA 58.637 37.037 0.00 0.00 0.00 3.33
1913 1977 7.816995 CCCTCTCTTCATCACTATATAAGCAAC 59.183 40.741 0.00 0.00 0.00 4.17
1914 1978 7.510685 ACCCTCTCTTCATCACTATATAAGCAA 59.489 37.037 0.00 0.00 0.00 3.91
1915 1979 7.013220 ACCCTCTCTTCATCACTATATAAGCA 58.987 38.462 0.00 0.00 0.00 3.91
1916 1980 7.475137 ACCCTCTCTTCATCACTATATAAGC 57.525 40.000 0.00 0.00 0.00 3.09
1965 2029 2.558795 ACGCATGCTTACCGATAGAGAT 59.441 45.455 17.13 0.00 39.76 2.75
2019 2083 5.389859 TGCATTTCACCTCCAAGTATTTG 57.610 39.130 0.00 0.00 0.00 2.32
2023 2087 6.418057 AAATTTGCATTTCACCTCCAAGTA 57.582 33.333 0.00 0.00 0.00 2.24
2066 2130 2.571653 TCAGGTAATGGAGTTCCTGGTG 59.428 50.000 9.66 0.00 45.07 4.17
2096 2160 0.603439 GGCAAACCAAACAGGCCATG 60.603 55.000 5.01 2.64 44.01 3.66
2135 2200 4.264083 TGCAGATTCTGGGAAGAAAATCCT 60.264 41.667 15.28 0.00 39.57 3.24
2146 2234 3.675228 GCAAGAACAATGCAGATTCTGGG 60.675 47.826 15.28 7.44 43.29 4.45
2172 2260 1.536766 GTAACAGTAAACCGCCAACCC 59.463 52.381 0.00 0.00 0.00 4.11
2185 2273 7.874016 TCATAAACGTGTAAATCCAGTAACAGT 59.126 33.333 0.00 0.00 0.00 3.55
2202 2290 4.127171 CGAATGGGGAGATTCATAAACGT 58.873 43.478 0.00 0.00 32.67 3.99
2203 2291 4.127171 ACGAATGGGGAGATTCATAAACG 58.873 43.478 0.00 0.00 32.67 3.60
2323 2412 7.060748 CACTTTACTATGTACGATATGCTTCGG 59.939 40.741 8.67 0.00 43.33 4.30
2336 2426 6.300703 AGTTGGCCAAACACTTTACTATGTA 58.699 36.000 22.47 0.00 41.61 2.29
2337 2427 5.137551 AGTTGGCCAAACACTTTACTATGT 58.862 37.500 22.47 0.00 41.61 2.29
2341 2431 6.724893 ATAAAGTTGGCCAAACACTTTACT 57.275 33.333 30.26 20.82 41.61 2.24
2342 2432 6.759356 ACAATAAAGTTGGCCAAACACTTTAC 59.241 34.615 30.26 15.46 41.61 2.01
2343 2433 6.879400 ACAATAAAGTTGGCCAAACACTTTA 58.121 32.000 29.98 29.98 41.61 1.85
2347 2437 6.079424 TCTACAATAAAGTTGGCCAAACAC 57.921 37.500 22.47 9.18 41.61 3.32
2348 2438 6.266558 ACATCTACAATAAAGTTGGCCAAACA 59.733 34.615 22.47 5.86 41.61 2.83
2349 2439 6.687604 ACATCTACAATAAAGTTGGCCAAAC 58.312 36.000 22.47 14.58 39.24 2.93
2350 2440 6.909550 ACATCTACAATAAAGTTGGCCAAA 57.090 33.333 22.47 4.55 0.00 3.28
2354 2444 7.094805 TGTCTCAACATCTACAATAAAGTTGGC 60.095 37.037 0.00 0.00 37.52 4.52
2366 2456 8.668353 TGCTAATTGAAATGTCTCAACATCTAC 58.332 33.333 0.00 0.00 45.48 2.59
2367 2457 8.791327 TGCTAATTGAAATGTCTCAACATCTA 57.209 30.769 0.00 0.00 45.48 1.98
2368 2458 7.627939 GCTGCTAATTGAAATGTCTCAACATCT 60.628 37.037 0.00 0.00 45.48 2.90
2369 2459 6.471519 GCTGCTAATTGAAATGTCTCAACATC 59.528 38.462 0.00 0.00 45.48 3.06
2391 2481 1.670811 CAATAAAGTAGGGCACGGCTG 59.329 52.381 0.00 0.00 0.00 4.85
2419 2509 0.901124 TGCAGTTGGGCAAACACTTT 59.099 45.000 7.64 0.00 41.65 2.66
2446 2536 1.486310 TGACTTCTCCTTGCACAGTGT 59.514 47.619 1.61 0.00 0.00 3.55
2483 2573 4.337060 GTTTGCCCGGCACCGAAC 62.337 66.667 13.00 10.71 38.71 3.95
2533 2623 3.738246 CTGTGCTGCTGCTGCTGG 61.738 66.667 27.67 15.67 40.48 4.85
2623 2713 8.134895 CCACCGTTTGCAAATATAATCAGTATT 58.865 33.333 16.21 0.00 0.00 1.89
2647 2737 8.408043 TCTCTTAAAATTCTGAGATTTTGCCA 57.592 30.769 14.90 0.00 39.05 4.92
2669 2759 6.907212 CGTGCATATTGGTCAGTTTTATTCTC 59.093 38.462 0.00 0.00 0.00 2.87
2673 2763 5.645929 TGTCGTGCATATTGGTCAGTTTTAT 59.354 36.000 0.00 0.00 0.00 1.40
2677 2767 3.052455 TGTCGTGCATATTGGTCAGTT 57.948 42.857 0.00 0.00 0.00 3.16
2693 2783 4.441792 TGTGGGATGATAATCACTTGTCG 58.558 43.478 0.00 0.00 0.00 4.35
2704 2794 2.959030 CCTCGTCTCTTGTGGGATGATA 59.041 50.000 0.00 0.00 0.00 2.15
2752 2842 7.198390 TGAATTAGCTCATGTAACCGTACTAC 58.802 38.462 0.00 0.00 0.00 2.73


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.